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Protein

Granzyme B

Gene

Gzmb

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

This enzyme is necessary for target cell lysis in cell-mediated immune responses. It cleaves after Asp. Seems to be linked to an activation cascade of caspases (aspartate-specific cysteine proteases) responsible for apoptosis execution. Cleaves caspase-3, -7, -9 and 10 to give rise to active enzymes mediating apoptosis (By similarity).By similarity

Catalytic activityi

Preferential cleavage: -Asp-|-Xaa- >> -Asn-|-Xaa- > -Met-|-Xaa-, -Ser-|-Xaa-.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei65 – 651Charge relay system1 Publication
Active sitei109 – 1091Charge relay system1 Publication
Active sitei204 – 2041Charge relay system1 Publication
Sitei229 – 2291Mediates preference for Asp-containing substrates

GO - Molecular functioni

  • serine-type endopeptidase activity Source: RGD

GO - Biological processi

  • apoptotic process Source: UniProtKB-KW
  • cytolysis Source: UniProtKB-KW
  • positive regulation of cell death Source: RGD
  • positive regulation of necroptotic process Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Keywords - Biological processi

Apoptosis, Cytolysis

Enzyme and pathway databases

BRENDAi3.4.21.79. 5301.
ReactomeiR-RNO-75108. Activation, myristolyation of BID and translocation to mitochondria.

Protein family/group databases

MEROPSiS01.091.

Names & Taxonomyi

Protein namesi
Recommended name:
Granzyme B (EC:3.4.21.79)
Alternative name(s):
Fragmentin
Natural killer cell protease 1
RNKP-1
Gene namesi
Name:Gzmb
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 15

Organism-specific databases

RGDi620018. Gzmb.

Subcellular locationi

GO - Cellular componenti

  • early endosome Source: RGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1818Add
BLAST
Propeptidei19 – 202Activation peptide1 PublicationPRO_0000027425
Chaini21 – 248228Granzyme BPRO_0000027426Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi50 ↔ 66PROSITE-ProRule annotation1 Publication
Disulfide bondi143 ↔ 210PROSITE-ProRule annotation1 Publication
Disulfide bondi174 ↔ 189PROSITE-ProRule annotation1 Publication

Keywords - PTMi

Disulfide bond, Zymogen

Proteomic databases

PaxDbiP18291.
PRIDEiP18291.

Expressioni

Gene expression databases

ExpressionAtlasiP18291. baseline and differential.
GenevisibleiP18291. RN.

Interactioni

Protein-protein interaction databases

IntActiP18291. 1 interaction.
STRINGi10116.ENSRNOP00000056412.

Structurei

Secondary structure

1
248
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi35 – 417Combined sources
Beta strandi49 – 568Combined sources
Beta strandi59 – 624Combined sources
Helixi64 – 663Combined sources
Beta strandi69 – 768Combined sources
Beta strandi88 – 9710Combined sources
Turni103 – 1064Combined sources
Beta strandi111 – 1177Combined sources
Beta strandi142 – 1487Combined sources
Beta strandi150 – 1523Combined sources
Beta strandi162 – 1687Combined sources
Helixi171 – 1777Combined sources
Turni178 – 1814Combined sources
Turni184 – 1863Combined sources
Beta strandi187 – 1915Combined sources
Beta strandi206 – 2105Combined sources
Beta strandi213 – 22210Combined sources
Beta strandi229 – 2335Combined sources
Helixi234 – 2374Combined sources
Helixi238 – 2458Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FI8X-ray2.20A/B21-248[»]
ProteinModelPortaliP18291.
SMRiP18291. Positions 21-247.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP18291.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini21 – 246226Peptidase S1PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase S1 family. Granzyme subfamily.PROSITE-ProRule annotation
Contains 1 peptidase S1 domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiKOG3627. Eukaryota.
COG5640. LUCA.
GeneTreeiENSGT00760000118895.
HOVERGENiHBG013304.
InParanoidiP18291.
KOiK01353.
OMAiDWECECH.
OrthoDBiEOG7RRF7Z.
PhylomeDBiP18291.
TreeFamiTF333630.

Family and domain databases

InterProiIPR009003. Peptidase_S1_PA.
IPR001314. Peptidase_S1A.
IPR001254. Trypsin_dom.
IPR018114. TRYPSIN_HIS.
IPR033116. TRYPSIN_SER.
[Graphical view]
PfamiPF00089. Trypsin. 1 hit.
[Graphical view]
PRINTSiPR00722. CHYMOTRYPSIN.
SMARTiSM00020. Tryp_SPc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
PROSITEiPS50240. TRYPSIN_DOM. 1 hit.
PS00134. TRYPSIN_HIS. 1 hit.
PS00135. TRYPSIN_SER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P18291-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLLLLLLSF SLAPKTEAGE IIGGHEAKPH SRPYMAYLQI MDEYSGSKKC
60 70 80 90 100
GGFLIREDFV LTAAHCSGSK INVTLGAHNI KEQEKMQQII PVVKIIPHPA
110 120 130 140 150
YNSKTISNDI MLLKLKSKAK RSSAVKPLNL PRRNVKVKPG DVCYVAGWGK
160 170 180 190 200
LGPMGKYSDT LQEVELTVQE DQKCESYLKN YFDKANEICA GDPKIKRASF
210 220 230 240
RGDSGGPLVC KKVAAGIVSY GQNDGSTPRA FTKVSTFLSW IKKTMKKS
Length:248
Mass (Da):27,326
Last modified:November 1, 1990 - v1
Checksum:i6F52089DDACCC88C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti98 – 981H → F AA sequence (PubMed:1732416).Curated
Sequence conflicti138 – 1381K → D AA sequence (PubMed:1732416).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34097 mRNA. Translation: AAA42055.1.
PIRiA43520.
RefSeqiNP_612526.2. NM_138517.3.
XP_002728303.2. XM_002728257.4.
UniGeneiRn.132115.
Rn.145789.
Rn.21395.

Genome annotation databases

EnsembliENSRNOT00000041430; ENSRNOP00000040429; ENSRNOG00000049976.
ENSRNOT00000059660; ENSRNOP00000056412; ENSRNOG00000045973.
GeneIDi100361468.
171528.
KEGGirno:100361468.
rno:171528.
UCSCiRGD:620018. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34097 mRNA. Translation: AAA42055.1.
PIRiA43520.
RefSeqiNP_612526.2. NM_138517.3.
XP_002728303.2. XM_002728257.4.
UniGeneiRn.132115.
Rn.145789.
Rn.21395.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FI8X-ray2.20A/B21-248[»]
ProteinModelPortaliP18291.
SMRiP18291. Positions 21-247.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP18291. 1 interaction.
STRINGi10116.ENSRNOP00000056412.

Protein family/group databases

MEROPSiS01.091.

Proteomic databases

PaxDbiP18291.
PRIDEiP18291.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000041430; ENSRNOP00000040429; ENSRNOG00000049976.
ENSRNOT00000059660; ENSRNOP00000056412; ENSRNOG00000045973.
GeneIDi100361468.
171528.
KEGGirno:100361468.
rno:171528.
UCSCiRGD:620018. rat.

Organism-specific databases

CTDi100361468.
3002.
RGDi620018. Gzmb.

Phylogenomic databases

eggNOGiKOG3627. Eukaryota.
COG5640. LUCA.
GeneTreeiENSGT00760000118895.
HOVERGENiHBG013304.
InParanoidiP18291.
KOiK01353.
OMAiDWECECH.
OrthoDBiEOG7RRF7Z.
PhylomeDBiP18291.
TreeFamiTF333630.

Enzyme and pathway databases

BRENDAi3.4.21.79. 5301.
ReactomeiR-RNO-75108. Activation, myristolyation of BID and translocation to mitochondria.

Miscellaneous databases

EvolutionaryTraceiP18291.

Gene expression databases

ExpressionAtlasiP18291. baseline and differential.
GenevisibleiP18291. RN.

Family and domain databases

InterProiIPR009003. Peptidase_S1_PA.
IPR001314. Peptidase_S1A.
IPR001254. Trypsin_dom.
IPR018114. TRYPSIN_HIS.
IPR033116. TRYPSIN_SER.
[Graphical view]
PfamiPF00089. Trypsin. 1 hit.
[Graphical view]
PRINTSiPR00722. CHYMOTRYPSIN.
SMARTiSM00020. Tryp_SPc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
PROSITEiPS50240. TRYPSIN_DOM. 1 hit.
PS00134. TRYPSIN_HIS. 1 hit.
PS00135. TRYPSIN_SER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "RNKP-1, a novel natural killer-associated serine protease gene cloned from RNK-16 cytotoxic lymphocytes."
    Zunino S.J., Bleackley R.C., Martinez J., Hudig D.
    J. Immunol. 144:2001-2009(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: T-cell.
  2. "Purification of a factor from the granules of a rat natural killer cell line (RNK) that reduces tumor cell growth and changes tumor morphology. Molecular identity with a granule serine protease (RNKP-1)."
    Sayers T.J., Wiltrout T.A., Sowder R., Munger W.L., Smyth M.J., Henderson L.E.
    J. Immunol. 148:292-300(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 21-53.
  3. "A natural killer cell granule protein that induces DNA fragmentation and apoptosis."
    Shi L., Kraut R.P., Aebersold R., Greenberg A.H.
    J. Exp. Med. 175:553-566(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE.
  4. "The structure of the pro-apoptotic protease granzyme B reveals the molecular determinants of its specificity."
    Waugh S.M., Harris J.L., Fletterick R., Craik C.S.
    Nat. Struct. Biol. 7:762-765(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 21-248 IN COMPLEX WITH E.COLI ECOTIN, ACTIVE SITE, DISULFIDE BONDS.

Entry informationi

Entry nameiGRAB_RAT
AccessioniPrimary (citable) accession number: P18291
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: November 1, 1990
Last modified: June 8, 2016
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.